Align candidate WP_106714834.1 CU100_RS01740 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00263.hmm # target sequence database: /tmp/gapView.177507.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00263 [M=385] Accession: TIGR00263 Description: trpB: tryptophan synthase, beta subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-192 623.5 0.0 8.7e-192 623.3 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106714834.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106714834.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 623.3 0.0 8.7e-192 8.7e-192 1 383 [. 18 410 .. 18 412 .. 0.97 Alignments for each domain: == domain 1 score: 623.3 bits; conditional E-value: 8.7e-192 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskkl.......... 63 g+fg fGG++v+e+l++ + el++ay++ak+d++fk+el+ l +yagrp+ l++a+ l++++ NCBI__GCF_003010935.1:WP_106714834.1 18 GMFGIFGGRFVAETLMPLILELQQAYDDAKNDPAFKAELQALSTHYAGRPSKLYYAEGLTRHVrqlareqgld 90 79*******************************************************9998753333333344 PP TIGR00263 64 ggakiylkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedver 136 ggakiy+kredl+htG+hkinn lgq+lla+r+Gk+riiaetGaGqhGva+at++a++gl c+vymGa+dver NCBI__GCF_003010935.1:WP_106714834.1 91 GGAKIYFKREDLNHTGSHKINNCLGQILLARRMGKTRIIAETGAGQHGVASATVSARFGLPCVVYMGATDVER 163 579********************************************************************** PP TIGR00263 137 qklnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevke 209 qk+nvfrm+llga+v+pv+sG+ tlkda+nealrdWv++vedt+y++G+a+GphP+Pe+vr+fq+vig+e++e NCBI__GCF_003010935.1:WP_106714834.1 164 QKPNVFRMKLLGAEVKPVSSGHGTLKDAMNEALRDWVSNVEDTYYLIGTAAGPHPYPEMVRDFQAVIGTEARE 236 ************************************************************************* PP TIGR00263 210 qilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkll 282 qile+egrlPd+++a+vGGGsnaiG+f++f++d +ve+ig+eagG+G+d e+h+a++s+G++GvlhG++t+ll NCBI__GCF_003010935.1:WP_106714834.1 237 QILEREGRLPDTIVAAVGGGSNAIGLFHPFLDDRQVEIIGIEAGGRGLDGEEHCASMSAGRPGVLHGNRTYLL 309 ************************************************************************* PP TIGR00263 283 qdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaalek 355 q++dGqi + hsvsaGldypgvgPeh++l +tgr++y+ + d+eal+a++l +++eGiipales+ha+a+++k NCBI__GCF_003010935.1:WP_106714834.1 310 QNKDGQILDGHSVSAGLDYPGVGPEHSWLRDTGRVSYVPVLDNEALDAFTLTTRTEGIIPALESAHAIAHAVK 382 ************************************************************************* PP TIGR00263 356 lapklkkdeivvvnlsGrGdkdletvak 383 +apk+++d+i++vnlsGrGdkd++tv + NCBI__GCF_003010935.1:WP_106714834.1 383 IAPKMAQDKIMIVNLSGRGDKDVHTVGQ 410 ************************9965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (416 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.47 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory